Marcus D. Hanwell's Blog

I am very pleased to announce that Avogadro has been nominated as a finalist in the SourceForge community choice awards this year. We are in the "Best Project for Academia" category, and I would like to encourage you to vote for Avogadro.

This is a real honour for all of us, and I appreciate all of you who nominated Avogadro. We are all pushing very hard on polishing Avogadro, getting ready for our 1.0 release. It would be absolutely amazing to see Avogadro win this award, so please vote for us.

There are also some other really nice projects in there too, such as Lancelot, ClamAV, phpMyAdmin and RepRap. So please take a few moments to place your vote, and tell your friends!

Update: You can vote even without a SourceForge account - just enter your email address and verify your vote.

Exactly two weeks ago today my son was born, weighing in at 8 lbs 13 oz and measuring 21 inches long. Louise and I have named him William Aaron Alexander Hanwell, our new addition has been thriving after a bumpy start. I would like to claim first foetal attendee of a KDE conference, getting him off to a brilliant start listening to some great technical talks in Jamaica. I know most people play classical music to their unborn children, but we like to be different I need to find him a KDE baby grow!

You can see him in the above photos just minutes after his birth, and a little more relaxed the next day in his hospital crib. Not wanting to be too run of the mill he was consistently breach, delivered by C-section and had his cord wrapped around his neck 2.5 times. Not a problem for that kind of delivery, but it would have been had we had the natural birth we were hoping for. As he was born in the US he also manages to get dual nationality (US by birth, UK from us), whilst his poor old Dad is still waiting to hear back about his H-1B visa...

I think three days prior Carsten's wife gave birth too, and I believe Mauricio will also be growing his family later this year. So the KDE Edu developers all seem to be expanding their families this year, I guess the greater question is whether this was a coordinated effort As with all true geek babies I will be setting him up with his own blog and online photo album, mainly so that our family and friends back home will be able to keep up with him as he grows.

So far I am really enjoying being a new father, although aware that this isn't the only big change over the summer!

Over the last few days we have been working on improving the look and feel of the Avogadro user interface. We owe both Qt Software and the Oxygen icon team a lot for making this process a lot easier. Avogadro uses quite a few Oxygen icons that we have taken and in some cases adapted slightly.

The sliver of screen shot above shows our tools tool bar, along with the tool and display settings buttons. We are pretty happy with the majority of the icons, which are (from left to right) draw, navigate, bond-centric manipulation, atom centric manipulation, selection, auto rotation (animated rotation about axes), auto optimise (continuous optimisation of the molecule geometry), z-matrix, measure and align tools.

I would really welcome any suggestions and/or icon submissions for the auto rotate (the spinny thing near the centre), and the auto optimise (the wand with the circle) tools. I think auto rotate is OK, but it would be better if it conveyed more of a three dimensional rotation. The auto optimise wand is perhaps the worst as it does not suggest optimisation of the geometry, but I am not sure what would. Do any of you more creative types have any suggestions?

I also wonder if there are nice icons we could use for tool and display settings, or a way to make those buttons smaller without losing discoverability. I look forward to hearing people's thoughts. As this is what people see when they first open Avogadro we would like to make the interface as inviting and intuitive as possible.

Yesterday I tagged the Avogadro 0.9.5 release, you can grab the latest downloads from here. Life has been hectic this last couple of months, and to be honest I have not gotten as much done as I would have liked. Still there are some great additions such as the experimental cartoon ribbon display ported by Tim from the Zodiac Zeden project.

Geoff also worked on getting more screen real estate for the actual display, after we bounced some ideas around over the last few months. I think that looks great, and have always tried to ensure the maximum amount of screen space was devoted to displaying the molecule. I still have a few more ideas, but fear I do not have the time to implement them. Geoff also added a new peptide builder and David has been working tirelessly on plotting spectra.

I have been working on decidedly less glamorous and less visual aspects of Avogadro. This includes improvements to our build system, I added the infrastructure required to find and build plugins/applications against the system installed Avogadro library. I also uploaded a few examples to GitHub, and David is actively working on an external plugin for a summer project.

I worked on getting a CMake project that included and compiled both Avogadro and OpenBabel. I then turned my attention to making a relocatable, self-contained app bundle for the Mac. This is working quite well, although there are a few parts of the build system I would like to clean up. It does mean we have relocatable applications that can run from a USB stick on both Windows and Apple systems now.

I crushed quite a few bugs too, worked on API improvements and fixed Noel's long standing feature request - to disable the visual cues when navigating around a molecule. The original Windows installer shipped with a data loss bug, when saving a molecule the original could be erased and you would be left with a zero length file. This was a Windows specific bug that slipped through, I spent half of today tracking this issue with a few other Windows bugs and updated installers have been uploaded (Tim made the Python enabled installer). Please ensure you update to Avogadro-0.9.5-win32a.exe or Avogadro-0.9.5-python-win32.exe. Hacking on Windows has to be one of my least favourite activities, and I need a couple of days away from that whole platform before I can go back and finish some of the work I have been doing...

We are pushing to a 1.0.0 release, targeted for July. We would appreciate feedback on the interface, bugs encountered, the public API that is installed along with any other suggestions or offers of help. Our translations are now doing very well too, and any help improving them further would be appreciated.

Enjoy the new release, another is likely only a week or two away as we crush the remaining bugs. I am also fighting to find time to implement a few more features I would really like to see in Avogadro 1.0.0.

I just got an email from Sourceforge about their community awards. If you are a user, fan or developer please vote for Avogadro in the Best Project for Academia category. They even provided me with a nice graphics to put on the page, you can just click on it to register your vote.

In other news lots of exciting things happening in Avogadro, hopefully I will find some time to blog about them soon!

The KDE GSoC sprint is over, and we have all returned to our respective homes. We lost a couple of people who had early flights on Sunday, I snapped a fairly blurred group shot Saturday evening, outside of the MIT Stata Center. After an intense day of hacking we headed out for food in the middle of a torrential down pour. We had some great Indian food, ice cream and then went candle pin bowling before they closed at midnight.

Sunday morning we got back into hacking pretty early on. We debated the merits of different editors, the role of desktop and internet applications and debugged a few issues with development environments. We also got Dunkin' Donuts coffee and some very tasty burritos. Sunday was cut short by flights, but Jeff very kindly ferried the two groups to the airport for flights at around 6pm and 8pm.

As I was in the second group we took the opportunity to walk into Boston from Cambridge and take a look around. As we crossed the river I took the opportunity to take lots of photos and stitch them together into my first panorama. I think it turned out quite well, I am just starting to get familiar with the software.

I spotted a few posts from Chani and Alejandro about the event too. It was great meeting you guys and I hope you all have a great summer of code!

We all arrived yesterday in Boston, got to know each other and did some hacking. Yesterday evening we all went to an iMax theater to see the new Star Trek movie. We have spent most of the day talking code and hacking in a small room in one of MIT's buildings.

It has been a pretty productive day, and it is always great to meet up with KDE developers old and new. Everyone is heading out at various points throughout tomorrow. Thanks to Jeff and Qt Software for making this event happen.

A week ago today we released Avogadro 0.9.4. If you would like to try out the new release then you can grab packages and source here. No pretty pictures this time as I am at the KDE GSoC America sprint in Boston, MA and only have my little Eee PC with me. I will see if I can remedy that when I get back home.

This week has been really busy. I have been working hard on getting an Avogadro, OpenBabel super project set up on the Mac. Then using the CMake functions to make a fully relocatable app bundle. This is really experimental right now, but if you would like to play with it then check it out in the downloads section. It is actually the 0.9.4 release with a few patches to our translation files and some other small fixes. It can be run from any directory, and contains Qt and OpenBabel.

There were a few problems with the 0.9.4 release we discovered a few days after the release was made. The main user visible issue is with the translation files not loading, and so we will hopefully get a new release out soon. This is already fixed in head.

In January I started looking for a job as my postdoctoral position at the University of Pittsburgh was due to end in September. I took a break from this to attend Camp KDE, the first KDE meeting held west of the Atlantic. I gave two halves of two talks (so a whole talk in total) where I talked about two things I work on in the open source world - scientific visualization and packaging.

Bill Hoffman also attended the meeting and gave a talk about CMake. While watching his talk (and I think the same happened while he was watching my talks) it clicked that Kitware would be a great fit. Once I got back to Pittsburgh I sent off a copy of my CV, and they very quickly set up some phone interviews. After that they flew me out to Clifton Park for quite an interview, if you get me over a few beers I might tell you all about it...

The more I learned about Kitware the more I liked it. Their language of choice is C++, they do a lot of scientific visualization, such as ParaView, work with national labs, academics and companies on interesting scientific problems. Then there are the software process, cross platform build, test and packaging projects. They even use Qt, and will likely use it more now the license has changed. Most of their software is released under an open source license too! I really got on with Bill and his family when I met them at Camp KDE, and came away with a very good impression of Kitware after the interview.

I accepted a job offer for the position of research and development engineer at Kitware in Clifton Park, NY. Due to being British, and various visa issues I will not be starting there until October (assuming all the visa paperwork falls into place). My wife and I are very excited about this opportunity at Kitware. So wish me luck, I am leaving academia after quite a long stay. Don't tell anyone at Kitware, but most of the stuff they want me to do I would gladly do in my spare time They are still looking for more developers, especially people with C++ and Qt experience if you are on the job market too.

I have been experimenting with Qt Creator since the first release. I have always preferred a minimal editor for development work, with my main needs being good syntax highlighting, the ability to switch between different files quickly and something that stays out of my way as much as possible. Previously I had used Vim, Kate and several konsole instances the majority of the time.

Recently I have been looking for something with better integration, and so had been slowly keeping an eye out for a lightweight IDE. My main requirements were something lightweight, good C++ support, ideally good Qt support and CMake integration. Over the weekend I tried the latest Qt Creator 1.1 release and was really impressed.

Seb Ruiz made a great post on Qt Creator 1.1 that summed up many of my thoughts, and gave a quick walkthrough. It was not immediately obvious how to import a CMake project, I was looking for an import project option. All that is necessary is to go to file and open. You can then open the base CMakeLists.txt file for your project and the CMake plugin will do the rest.

From there on in you get great integration with the build system, version control (Git and friends), and your friendly GDB debugger. Under projects you might want to quickly add -j5 (if you are lucky enough to have a quad core machine) to the additional arguments input for make, and select the main executable target for your project if you also have several other executable targets (unit tests etc).

The first time you debug a project you will be prompted to build the Qt debugger helper. Then the integration with GDB really wins over using GDB directly, or using ddd which I had been using more and more recently. I would highly recommend trying Qt Creator if you are looking for a lightweight, cross platform IDE. There are certainly other great IDEs out there, but I think that Qt Creator is a great fit for my development style (and may be yours).

Recently, Luca made a post comparing the speed of CMake and autotools in which some timings were posted. I have to say that I am not sure I agreed with the conclusion and have had a very different experience with the projects I am involved in. As with anything your mileage may vary, and I have not looked at Wesnoth.

I think it is questionable at best to include the time it takes to build CMake, but not autotools. Seems like this is a one time cost and the build time is not that high for either. All tests were performed on my quad core Gentoo box at work. Each step is for the first cold run as would normally be the case when compiling Open Babel from source. The make step used `time make -j5` and I have listed the real time in each case.

The timings are shown in the table below. They seem somewhat similar to the experiences of the QGIS developers who made this move quite some time ago. All times shown are in seconds and are the real time reported by the time command.

For those interested, on this system the total CMake compilation/installation time (cmake-gui disabled) was 1 minute and 54 seconds. The compilation/installation time for automake, autoconf, libtool, m4 was 2 minute and 14 seconds. I am not sure how relevant either of those times are, other than to show neither of them take that long to compile and install. Gentoo users/developers may or may not have CMake installed, most other developers will install the binary packages for either one and are likely to be much more interested in how well it integrates with their development environment, compile and install times.

As a developer I prefer CMake, and have been using/maintaining the CMake based build system for Open Babel for over a year now. It was originally contributed by the KDE Windows porting team, but I found that I spent less time waiting for it to do things when I was working on code too. Add to that the extras CMake comes with, such as CTest, CDash and CPack I think it makes a very attractive option for many projects. I am also hoping that it will allow Open Babel to drop maintaining a totally separate build system for MSVC.

I am sure the Open Babel autotools build system could be optimized (I never tried), but when you add in the additional benefits mentioned above, support for multiple targets such as makefiles, XCode, MSVC, Eclipse etc, one shared language/syntax for all build files and an increasingly polished competitor to autotools, I honestly think it is a sensible choice for projects to move to CMake. There are a few less well known features such as Fortran module dependency parsing that I think are fairly unique and valuable, in scientific coding at least (and I have used the Fortran module dependency parsing at least once and was pleasantly surprised).

Full disclosure: I recently accepted a job offer with Kitware, and will start in the Fall assuming all the visa paperwork falls into place. The opinions expressed here are my own. I think it is great to discuss issues like this objectively, and hope to be a part of making CMake a better build system. As with most software - there are areas that need improving.

Yesterday, on April 1, we tagged and released Avogadro 0.9.3 exactly one calendar month after 0.9.2 was released. This has been quite a big month for Avogadro - I took it to the APS March meeting and the Q-Chem workshop. To the left is a screenshot of the latest release showing the electron density of a vitamin C molecule with the approximated electrostatic surface potential mapped onto it.

We made quite a few fixes and improvements leading up to the APS and Q-Chem meetings. The highlights are in the release notes. Some of my favourites are the animation of molecular vibrations, plotting of IR spectra, improved rendering/handling of surfaces including meshes with colours mapped to their vertices. The Windows build is also fully relocatable, meaning it can even run off of a USB stick. I am hoping to do the same for the Mac and Linux builds too. I made several improvements to the super cell builder, surfaces and even made a start on a z matrix editor (not ready yet).

To the right is the ray traced image of a larger molecule and one of its molecular orbitals. The POV-Ray rendering code has also seen quite a few improvements. I have been experimenting with generating movies from POV-Ray rendered images too. I am planning to make improvements to our build system on Windows and Mac in order to make packaging easier. My main focus is still Linux development, but so many people insist on using other operating systems. Other more exciting things include producing videos of molecules rotating, vibrating, trajectories and using GLSL to improve the rendering performance with big systems (>25,000).

We would appreciate feedback on this release from the wider community. I am really pleased to announce we have gained at least one new contributor this month, David Lonie, who worked on the new IR spectra plotting code. I have made a new ebuild for Gentoo, prepared a Windows installer, Geoff has made a new Mac package and there is ofcourse source. I am sure other distros will have packages ready soon too. Hope you enjoy the graphics - videos to come soon!

So last week was extremely busy. The APS March Meeting was held in Pittsburgh and Q-Chem held a workshop on Q-Chem at the end of the week. I presented a poster on Avogadro (shown below), met lots of interesting people and got lots of new ideas for both research and Avogadro.

As we push towards making a 1.0 release of Avogadro, getting feedback from users in the scientific community is extremely important. As Q-Chem chose to use Avogadro as the builder/visualizer in their workshop I had the opportunity to observe new Avogadro users interact with our application for the first time. I also had the opportunity to help them overcome some initial issues and gained a few new insights.

I was very pleased to meet people at all stages of their career who were very interested in having an open source application that can provide a framework for building and visualizing molecules. I also realized that two of the most sought after features in Avogadro right now are the capability to easily make movies, and a z-matrix editor. People loved the ray-traced images of surfaces, coincidentally I received a request from someone in the press wanting to use an image I put up on my blog last year of ray-traced benzene molecules.

I look forward to hearing from some of the new users we gained in the last week. It is great to see Avogadro receiving more attention. I have started to work on the z-matrix editor and spent the weekend experimenting with movies - more to come soon!

So last weekend Louise and I went on our first big road trip to Canada. Neither of us have been to Canada before, and with Benoit now living in Toronto it seemed like a great opportunity to go and catch up. Back in July 2007 I visited Benoit in Paris during my GSoC where we met for the first time in person. Now, two years on we met for the second time in person and introduced our partners to each other too.

We left at around 4pm on Friday, I think we crossed the border at about 9pm and got almost all the way there before getting lost in Toronto. Our friend's GPS failed us once we crossed the border and Toronto is a pretty big place. I think we finally arrived just before midnight, tired after the long drive. The next day we drove back down to almost the border to check out the Niagara Falls, which we had never seen before. It rained almost the entire day but we still had a really nice day out.

As well as checking out Niagara Falls on the Canadian side in the rain, we found some very expensive shops in Niagara on the Lake, I bought some maple syrup and some maple spread (still not quite sure what to do with that). We discovered that if you get bored of the main attraction you can always check out one of the many casinos too.... We decided to forgo the gambling and instead headed back to Toronto.

Once we had dried off a little we all headed out to get some dinner in Toronto's chinatown. We enjoyed some great Vietnamese food and compared notes on moving continents, life in academia, Google Summer of Code and life in general. It is great to still be in touch with many of the people I made friends with during my Google Summer of Code and I hope others get as much out of it as I did.

On Sunday we lost an hour to daylight savings time, wish we could stop doing the clock change thing twice a year... We decided to head back as Louise was tired (she is conducting a geek cloning experiment for me). It rained for most of the drive back too, we did another border crossing and got back home at around 7pm. I do not think our carbon footprint is looking great for the weekend but it was great to catch up and see where Benoit is living now. My thanks to Benoit and Irene for being such great hosts.

Back to work this week, preparing for a big conference next week. I still love to travel, it was great to avoid the airports for once!

I just finishing tagging Avogadro 0.9.2 earlier today. I possibly procrastinated on tagging this one a little as February has not been my finest month. I didn't see any reason to make another release in that hellish month when I could wait a day. This release is a little earlier than we had scheduled, but it contains lots of bug fixes and improvements along with a couple of new features.

Among the highlights I tracked down our orphaned tools and extensions, so Avogadro closes down far more gracefully now than it once did. I went hunting for memory leaks and QObjects with no parents. I added some initial support for building supercells such as the zeolite structure shown in the screenshot. I also fixed some bugs with electron density calculation and this works much better and faster now. I also improved the Linux desktop user experience by adding a .desktop file, icon and mime type associations. Looks very swish.

I built a new Windows release without Python, Tim will put one up with Python support soon, bumped the Gentoo ebuild as 0.9.1 was bumped by someone else and it could not locate its plugins. I have made a number of improvements to our plugin loading to ensure that it is relative to the binary location. This should make relocatable binaries on all platforms quite feasible. March is a busy month but I hope to be able to make some more big improvements. If it goes as badly as February I may consider hibernation as an option though!

I will be presenting some of this work at the APS and a quantum chemistry workshop in March too, both here in Pittsburgh. We always love to have feedback, bug reports, patches or be invited to give talks at conferences in far off places! Here is hoping for a better month...

We continue our push forward with Avogadro with the release of Avogadro 0.9.1 on 16 February. There are lots of new features that made it in recently and we are still stabilizing many of them. This release has featured lots of experimentation with CPack, along with me getting more familiar than perhaps I ever wanted to with Windows packaging. CMake makes things easier but there are some things it cannot fix, such as the manifest issues we hit.

This is the second of our final beta series before our 1.0 release. We hope to make a release roughly once a month until we release Avogadro 1.0. During this period some new features will be added. Our main focus will be on improving the API, fixing crashers, ensuring all platforms have stable packages with full functionality and improving fault tolerance. To this end we will be adding to our (currently) quite small test suite and making use of CDash in order for all developers to be able to see issues on all targeted platforms.

Since the release I found a few small bugs and so already want to make a new release. I fixed a bug when calculating electron density cubes from formatted checkpoints - it was one stray line of code! There is a super cell builder that can do rebonding on the super cell in the works and I recently committed some code to use relative paths to find our plugins. This seems to work really well and with a little tinkering should allow us to run off a USB stick without installation.

While working on our Windows build I realized I have been neglecting our Linux build a little. So I have an avogadro.desktop file and some mime type files to give us a menu entry and associate with some file types. I may not have chance to finish them up and commit until I get back on Sunday.

On that note I will likely be offline until Sunday/Monday. I have my first big job interview tomorrow - wish me luck! Like several people on Planet KDE I am currently in the market for a job. I am going to be all mysterious and not give any more details, other than to say I am excited and nervous!

So it is Friday the 13th... At about 5am this morning my server emailed me to tell me one of its disks was down... It is all RAID1 (apart from swap) and so it is mostly OK. I think having half its swap removed upset it quite a bit though, and so almost all services died. I think they are all back up and running again, but if you emailed anything in the last day or so you might want to resend it.

This week has not been my finest - hopefully next week will be much better! Here's hoping nothing else went terribly wrong this week, and that it is just the disk and not the whole server that is having trouble. So much to do, I did not need this.

I am very pleased to announce that Avogadro was recently featured by Qt Software on their Qt In Use page. I worked with Alexandra Leisse at Camp KDE on getting the page ready and we recently got the rest of the screenshots and videos prepared.

Check out the Avogadro Qt page and some of the features we were able to implement very rapidly thanks to the great API provided in Qt 4. The Avogadro development team is very pleased to be featured by Qt. Many of the features in Avogadro would not have been possible to implement in such short timescales without Qt. As I said on that page, we have made extensive use of the Qt plugin framework to dynamically load almost all functionality at runtime.

There are a few problems with our Windows installer, which was originally a hand crafted NSIS installer. There is a preview of a new CPack generated installer. You can get it here if you are cannot wait to try it on Windows. It lacks Python support right now as that brings in quite a few extra dependencies I have not had time to compile on my Windows virtual machine yet.

I am going to shock you all and admit that I am not a Windows programmer! I do however know quite a bit about cross-platform development and have now learnt the joy that is the manifest in Windows development. It seems that DLL hell is now a thing of the past, all hail manifest hell. A week ago I was not aware of these wonderful little files and this post is an attempt to document what I learned while packaging Avogadro for Windows.

After listening to Bill's talk at Camp KDE I was convinced that it really was a good idea to use CPack to package Avogadro. So when I got back home I spent a day or two getting a Windows development environment set up for Avogadro. We have several dependencies such as Qt and this post documenting a bug in the Visual Studio 9 service pack. So I edited the manifest and lied about the version of the DLLs - it believed me.

Next I found that none of our plugins would load. They are Qt plugins that implement most of the functionality in Avogadro. I found a very long thread on this subject, the crux of which is that the embedded manifests are causing Windows to look for the runtime libraries in the plugin directory. Copying them did indeed work but was not optimal. I found that by adding set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /MANIFEST:NO") to our CMakeLists.txt manifests were no longer made for our plugins (which are loadable modules).

So all is quite well with our Windows build now I think. If you would like to try out a new Windows installer, then please download it from here and let me know if it works for you. I have tested it on Windows 2000 and XP virtual machines. This is not the final installer, I need to add some extra data files for OpenBabel and ensure I got the other dependencies right.

If anyone with more Windows experience knows of better solutions please let me know. CPack is absolutely awesome, it seems a shame that the deployment of applications is made so difficult. I know that plugins are not as widely used and so hopefully this post will add to the collective knowledge indexed by Google.

I made a new Avogadro screencast earlier today, trying new formats and preparing a showcase of features in the recent 0.9.0 release. Unfortunately, due to an API change in Eigen this release only builds with eigen-2.0_beta6. The sources in git work with the recently released eigen-2.0, and I will try to make a new release in the near future.

The video shown above, is also available on YouTube, but the encoding does not look as good as on blip.tv. It shows off several of the features present in the current Avogadro release. There are a few issues with the Windows installer, which is another reason to put a small bug fix release out soon.

I have been putting my newly acquired Qt takes to compile in a Windows virtual machine, I do have a working Windows build environment now. I got CDash working for our project, even without unit tests it is great for flagging build errors/warnings on multiple platforms. I also have CPack generating our NSIS based Windows installer now. There are a few rough edges remaining that I hope to iron out soon, but I think our packaging just got a lot easier - thanks to Bill and Kitware.

Things have been really hectic since I got back from Camp KDE. Had a great time, met lots of really interesting people, did not sleep very much (need to take ear plugs next time) and found my Eee PC with KDE 4.2 (rc at the time) worked great the whole week, and it is so light.

When I got back I found out that our espresso machine broke, and the electronics shop declared it a lost cause earlier today This has meant a serious espresso shortage since my return! Why do they always concentrate on redundant power systems for the clusters, but not redundant espresso systems for the researchers???

So really busy right now, hopefully good news coming soon on several fronts - keep your fingers crossed! I am loving KDE 4.2, CMake and Qt but in dire need of espresso products